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Structural Biochemistry and Bioinformatics

Introduction to Computer for structural biology/bioinformatics course

In this course we will use linux, which is a frequently used free operating system. However none of microsofts products work on linux. Linux is a dialect of UNIX. During the two first days you should familiarize you with unix.

When you use the computer you should distinguish between using the graphical interface and using the command line. Many programs can be started by clocking with the mouse, however other programs can only be executed using the command line. When we refer to the command line wer talk about a "shell", which actually is a program that interprets what you type on the command line.

The Shell

The default shell used on our computers is bash. Bash is very powerfull and can actually be used to write complete programs. This is often referred to as shell programming. Another useful features of bash is the auto-completion (performed by pressing the tab key. If you press the tab key twice and answer y to the next question you get a list of all the commands that you can run. Similarily if you type a command (for instance ls) you get alist of all files in the current ditecrory.

The shell is extremely usefull for automatic simple things, such as starting a program doing almost identical things many times. You will need to know how to do the basic shell programs.

Tutorial

This is an excellent introduction. Read it.!! Read this tutorial After this you should be familiar with the following commands:

After reading the tutorial you should be able to pass these assignments.

Graphical interface

The graphical interface on almost all Unix machines are based on the X11 protocol. This protocol makes it possible not only to open graphical programs from the local computer but also from another computer. You can try this by typing ssh computer_name and then type xterm to start a new terminal window from the other computer.

Graphics environment

X11 is just a protocol specifying how to draw things on the screen. It does not define how windows should be controlled. For this it is necessary to run a window managar/desktop environment. In this course we will use KDE and/or gnome

Utilities

Swiss PDB viewer

Netscape

Many assignments can be done by using netscape, if you have not used netscape before familiarize you with it. However it should work exactly as it does on a windows machine.

Email

You should give your email adress to Derek. If you do not have one you can get a temporary email address from the biocchemistry department.

Make your own home page

Now it is time to create your own home page. It is easiest done by using netscape. Just select edit page and place the file in ~/public_html/index.html

1. Now your file should be available from the following URL http://n-a.biokemi.su.se/~username/index.html

Make a personal home page, tell who you are and what is fun.